Summary across 15 ENCODE cell-lines

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The transcription factor binding site predictions presented here are obtained from data generated by the ENCODE project. In particular we use DNase-seq data obtained in 15 cell-lines by Greg Crawford at Duke University (see details and data release policy at the bottom). We generated maps for each of the following cell-lines:

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Methods

DNaseI HS data: (From UCSC "Open Chromatin" track)
The data was generated for the ENCODE project at Duke University's Institute for Genome Sciences & Policy (IGSP): Alan Boyle, Lingyun Song, Terry Furey, and Greg Crawford. Cells were grown according to the approved ENCODE cell culture protocols. DNaseI hypersensitive sites were isolated using methods called DNase-seq or DNase-chip (Boyle et al., 2008a, Crawford et al., 2006). Briefly, cells were lysed with NP40, and intact nuclei were digested with optimal levels of DNaseI enzyme. DNaseI digested ends were captured from three different DNase concentrations, and material was sequenced using Illumina (Solexa) sequencing. DNase-seq data were verified using material that was hybridized to NimbleGen Human ENCODE tiling arrays (1% of the genome). Multiple independent growths (replicates) were compared to verify the reproducibility of the data. A more detailed protocol is available here.

CENTIPEDE: This is a method developed by Roger Pique-Regi, Jacob Degner, Jonathan K Pritchard and others at Univerisity of Chicago that uses PWM information plus experimental data such as DNase1, histone marks or FAIRE to infer transcription factor binding sites with high specificity. Software and more details are available here.

Data Release Policy

The CENTIPEDE predictions are freely available but are subject to the ENCODE release policy. Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page for the "Open Chromatin" track. The full data release policy for ENCODE is available here.